# Short Tutorial

In the following we explain how to reproduce the datasets of the respective manuscript.

## 1. Rejoin files

Run the following command to re-join the splitted datasets:

    cat 1.1micron_10cmH2O_rawdata.zip.a* > 1.1micron_10cmH2O_rawdata.zip

Adjust the command accordingly to re-join all available datasets.

## 2. CT reconstruction

CT-reconstruct the projection datasets (e.g. with TomoPy). Each dataset is composed of 30 *dark images*, 100 *flat-field images*, 901 *projection images* and *100 post flat-field images* at the very end.

## 3. Run 3D rigid transform

Run the Matlab script `rigidTransform3D.m` to create cropped and aligned subvolumes. Adjust the correct file names in the script before running.

## 4. Segmentation/Processing

Finally, we continue with the processing as described in the manuscript. 